Because most of the island's hotels are seperated from the actual island itself, the ferry system in Bora Bora needs to be very comprehensive. During our stay on the Bora Bora Nui, which is on a motu (island) off the main island that is home to Vaitape and other villages, we had to take the ferry into town if we wanted to get to an off-resort restaurant or shopping center.
I would also be careful to get an updated ferry schedule when you arrive, as there was a gas shortage on the island when we were there, so they cut many of the ferry times!
There is a free shuttle service run by the airport to the main dock in Vaitape. The boats leave for Vaitape village about 20 minutes after your flight arrives and it takes about 20 minutes.
Check-in time for departure is 1.5 hours before each scheduled flight departure.
Arrivals and departures by plane in Bora Bora are from the motu, where the airport is located. You then take a shuttle boat on the lagoon from the airport to downtown (Viatape).
This is a lovely way to admire Bora Bora, because the plane reach the island too fast. The entrance to the port is also wonderful.